The Clone Wars
by Padfoot-001
Summary: The survivors of atlantis are at war with a new enemy, there only hope is an unborn child, but with the jumper fully restored perhaps they can do one better and get the real thing, John Sheppard. Provided he's still alive.


Note: And it's time again for another story. This one promises to be action packed with plenty of Shweir and a twisted, confusing sort of story line. Now make sure you tell me what you think. I like to know before I continue and get too far into the story. The rating may go up in later chapters. And don't let the title fool you, it has nothing to do with StarWars.

Disclaimer: I don't own stargate or it's character.

**The Clone Wars!**

**By Padfoot001**

Rodney McKay waited in silence behind the large pile of boulders he hoped would allow him to remain unseen untill the right moment of attack. His shaking hands were resting on the trusty P-90 that had shot down many of their enemy before and hopefully many more. Eyes tightly closed and breathing as steady as could be managed, he listened out for the first approuching steps of the enemy.

The light breeze was rustling the leaves around them with great delicacy, the only sound so far, other then the soothing breathing coming from the person that was crouched down next to him.

If someone had of told him a few months ago that he and Elizabeth Weir would be fighting, with confidence, in one of the greatest battles of all time, he would have simply laughed in their face and denyed that day would ever come. But sure enough, here they were, side by side, ready for anything.

She was usually a comfort to him, her presence always made him feel stronger. Fighting with someone, a friend, was always better then fighting alone. But lately the very knowledge of her on or near the battlefeild made him uneasy and sick to the stomache. There was no way of twisting it; she shouldn't have been anywhere near danger, she was too important, everything was resting on her shoulders. She was Plan A, the only plan, there was no Plan B, it was vital that she survived. Yet here she was sitting next to him, prepared to die, if that's what it took.

It was her choice, it always was. Wouldn't have mattered if he had shouted and yelled or confined her to a place where she could never be harmed, because she would find a way ... she always did.

There was the sound of dry leaves being crushed under heavy footing and Rodney, temporarily destracted, immediatly snapped back to where he was. His eyes wide open now, his P-90, matching Elizabeths', at the ready. He listened longer ... something was wrong. There was supposed to be more, but it only sounded like one approuching. He chanced a glance at Elizabeth, her fingers fidgeted over the trigger on her weapon, hands shaking slightly. No matter how many fights she had been in, she still acted as though each one was her first.

Silence surrounded them now, it wasn't right. Rodney was tempted to peak over their sheild of rocks, but he knew better. The enemy could be waiting right there with a weapon pointed straight at his face. _Think Rodney, what would Sheppard do? _Again he looked down at Elizabeth and wondered as he did almost every day how different it would all be if Sheppard had of been here instead of him -

'They're not coming.'

The sound of the voice was all that they needed, in a frenzy both he and Elizabeth spun around and aimed their guns at the culpret, ready to shoot. The mans arms immediatly shot up in the air in a surrender pose as the two of them held their fire at his panic stricken face.

'Zelenka? What the hell are you doing here?' Rodney kept his weapon on the familiar man, as did Elizabeth. They knew better then to assume it was _their_ Zelenka, the _real_ Zelenka.

'W-wait ... look, I'm just going to show you my wrist,' he watched Rodney carefully as the man nodded relunctantly. He couldn't shoot in case it was really Zelenka, but if it was an imposter he could be giving him easy access to summon a weapon. Tensing, Rodney watched the man slowly roll up the sleeve of his blue shirt. There, as clear as it should be was the Atlantis tatoo, the same symbol that was on the sleeve of their old uniforms, the symbol that meant this was indeed the real Zelenka.

Rodney let out a sigh of relief and dropped his weapon, he could see Elizabeth do the same. Zelenka rolled his eyes, dropped his arms and slumped over as he exhaled a breath he had obviously be holding in since Rodney had pointed the weapon at him.

'What are you doing here? You could have been killed!' Weir exclaimed, still in a hushed whisper as though someone whom wasn't welcome could overhear them. A foolish plight concidering all the action would have allerted any nearby to their position already.

'There's no need for that,' Zelenka said, in regards to her whispering. 'As I said before they're not coming. What men they had left departed from this planet. Carson sent me out to get you because ... well, he has a plan and if we're going to do this, we need to do it now. Whilst the clones are taking a recess of sorts.'

Rodney and Elizabeth looked at each other sceptically. A second plan would be perfect, but why hadn't Beckett spoke to them about it before. Neither one wanting to wait around any longer they stood and walked with Zelenka back to the Atlantis Command Base.

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Carson Beckett paced around in his office, waiting patiently for Rodney and Elizabeth to return. For once he knew that they would, that they hadn't been killed in battle - simply because there had been none this time. When the ships over head had beamed up all the men they had swarming around the planet, he couldn't believe his luck. Perhaps they had given up looking for their hideout. That was at least what he had hoped. They could also have been recalled to recieve a new battle stratergie, one that was a sure win. Nevertheless, this was the first real break that they had ever been given and they couldn't afford to waste it ... not now that _it_ was ready.

Despite himself the doctor stopped pacing and allowed himself a grin as he leant against the dirt walls of his office. Finally they had another Plan, finally they could have a little bit of hope. Their lives no longer depended on that of an unborn infant, they could do one better now. They could have the real thing.

'John Sheppard, I hope your alive,' he said, starring at the dark and dirty ceiling above him. 'Because you're all we have left.'

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Elizabeth hurried along after Rodney and Zelenka, she pushed herself, trying to breath easy as she did, but lately it had been a lot harder. The lack of sleep and all the fighting only added on to the natural exhaustion she was feeling in her current state. But she couldn't let them see her weak, not only for their sake, but for hers, she couldn't allow to see herself weak, she needed to be strong, or at least think that she was.

Finally, up ahead, she could see the kink in the enormous rock face. Together they entered the hidden cave. Perfectly hidden due to the cloaking technology they managed to keep a hold of. Only those that already knew where it was could find it, unless it was discovered by mistake. Once inside they followed the dark tunnel deep under the earth untill, finally they could see the lights of their underground city fighting through the blackness.

They exited the tunnel and stumbled into a giant underground gate room, a room leading off to many other corridors where what people they had left lived. It was an underground replica of the main part of the beautiful city of Atlantis that they once inhabited. It had been home for countless months now and it had kept them well hidden for their entire time there.

'Quickly, we must find Carson,' Zelenka announced the moment they had arrived and he began leading the way to the good doctors office. Elizabeth took a moment to catch her breath before she followed. As they walked she was greated by a number of Athosian soldiers, who smiled in delight that she and Rodney had come back alive.

The three of them made their way past their StarGate. Elizabeth looked at the thing in silent admiration, as she always did. Many lives had been sacraficed to get that particular StarGate and it was practically of no use to them. They couldn't use it for fear of being discovered by the enemy's superior tracking devices', but at least if an emergency presented itself, it was always there if they really needed to use it.

Once they reached Becketts office, the man waisted no time in explaining his full-proof plan to them.

'It's ready,' was the first thing he said to them as they walked through the door. 'The Puddle Jumper we picked up from the ruins ... it's up and running.'

Elizabeth looked at the smiling Rodney and joined in. 'Wow, that was fast. Nice work ... and I take it you have a plan already -' she asked remambering how excited Zelenka had been to tell them.

'Yes. The Cloners couldn't have chosen a better time to re-group. Now that the Jumpers ready we can get someone out there -' he pointed up at the ceiling '- and find us some much needed help.'

Letting a sigh of relief escape her, Elizabeth wearily slumped in one of Carson's chairs. But Rodney stepped forward.

'But what about the time travelling components? I mean they weren't fully tested yet and there's always that -'

'Rodney!' Beckett interupted the mans predictable rant. 'Rodney ... it's ready. Unfortunatly we haven't been able to test it yet, but from what I've been told, everything is re-built and restored as it should be.'

'Then we'll test it ourselves,' Elizabeth said, finding her legs and standing up again. 'If the Cloners are taking a break, then we make our move. What better time to make sure it works then right now when we need it the most.'

'I knew you'd say that,' Beckett grinned.

Elizabeth looked to Rodney. He had his head down and was yet to say anything further. He had to agree to the mission, he was the only one left that could fly the jumper now.

'This may just work,' he finally stated, looking up at them. Elizabeth smiled again and eagerly made for the door.

'Right, then we're off ... right now, we can't afford to waste any more time, we know what we have to do, we've been waiting for this chance from the beginning. So lets get going.'

But before she would make her way to where the Jumper was being kept she felt a tug on her arm. Turning around she came face to face with Becketts pleading eyes.

'Elizabeth, you can't go. You have to stay here.'

'What?'

'You heard me. If this fails, you're all that's left.' Beckett watched her closely. She didn't like hearing it, but she couldn't go. If something should happen whilst they were gone and she died, then the whole war was over.

She wanted to protest, more then anything, but he was right, she couldn't risk it. Instead she made to see them off.

It only took them a few hours to have everyone ready. Beckett was needed in the city in case of an emergency as was Zelenka, so in the end Rodney and a small team of Athosians were set and ready to depart. The biggest risk was activating the StarGate, the Jumper couldn't fly out of the base so they would have to send him to a deep space StarGate in order to exist safely.

'Good luck Rodney,' Elizabeth muttered softly as she watched the Jumper fly perfectly through the open Gate. The Gate shut down once the team disappeared through and everyone waited for weapon fire. Surely the Cloners got a signal from the opened gate ... but there was nothing.

'You should get some rest,' Carson said gently, appearing by Elizabeth's side. 'Unfortunatly there's nothing we can do now but wait.' Elizabeth nodded serenly then headed off to her quatres.

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Rodney flew the Jumper around just to get the feel for it once more. It had been a while since he had gotten to fly the thing and he wanted to make sure everything was in working order. The Athosian soldiers were company enough for the man, but this was the first time he had been on a mission without Elizabeth or Carson and he felt slightly empty. But with any luck he would be seeing them all again soon in much happier conditions, he just had to make sure not to send them all too far back in time. About a year should do it, anymore and they may yet to be on Atlantis, any less and they would probably be in the same position as they were.

Suddenly the ship was plummeted into darkness as a massive ship came out of hyperspace above them. Rodney gasped as he saw the deep black underbelly of the Cloners lead ship.

'Quickly, before they pull us in,' one of the Athosians yelled at Rodney. Snapping out of his surprise Rodney checked the console then made the final move.

'Hang on,' he said as he took the plunge into sending the space to the old Atlantis.

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AN: I know, I know ... okay I don't. So review and tell me please. Lol, hopefully it wont be too confusing, it will be for a while, but slowly it will start to make sense, I promise you. Yeah so let me know, I wanna see what you think. And no spoilers, so dont ask me. Im not telling anyone anything, lol.


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